preprocess_fp_psm – prolfquapp

preprocess FP psm, filter by purity_threshold and PeptideProphetProb

Description

preprocess FP psm, filter by purity_threshold and PeptideProphetProb

Usage

preprocess_FP_PSM(
  quant_data,
  fasta_file,
  annotation,
  pattern_contaminants = "^zz|^CON|Cont_",
  pattern_decoys = "^REV_|^rev_",
  purity_threshold = 0.5,
  PeptideProphetProb = 0.9,
  hierarchy_depth = 1,
  nr_peptides = 1,
  parse_fun = tidy_FragPipe_psm
)

Arguments

quant_data path to quantification data file(s)

fasta_file path to fasta file(s)

annotation annotation list from read_annotation

pattern_contaminants regex pattern for contaminants

pattern_decoys regex pattern for decoys

purity_threshold purity threshold for filtering

PeptideProphetProb PeptideProphet probability threshold

hierarchy_depth hierarchy depth for aggregation

nr_peptides minimum number of distinct (stripped) peptides per protein (>= 1, default 1)

parse_fun function for parsing PSM files

Value

list with lfqdata and protein annotation